Good tip about the fillet affecting the alignment. But it's easier to just chamfer the hole with a counter-sink bit....unless you forget to do that before the top and back are glued on

There are short, hand-held chamfer tools that fit easily into the sound-hole should you forget. I don't know everything about fasteners, so maybe it's not an issue, but would rather avoid introducing a stress riser or other weakness at the joint of the head and shaft.

This thread reminded me of a long standing question that's been rolling around in the back of my mind for a while. How much pull is actually exerted on the neck bolts? Because the strings pull in a line that is so close to the body, the majority of the string tension is pulling the neck into the body and only a small part is trying to rotate the neck upwards. If I remember how to do vector analysis of force diagrams properly from college physics, then assuming a 24.5" inch scale and total string tension of 160 lb, the upward component of the force at the nut is only around 2.5 lb. Using the 14th fret as the lever fulcrum point, the ratio of the length of the neck from the nut to the neck body joint to the distance from the top surface of the body to the lower bolt in the necks of my guitars gives a lever arm effect of about 5 to 1. So, if I had only the bottom bolt installed, the outward force on that bolt would only be about 12.5 lbs. I doubt that two of your bolts with the bevel removed would be in much danger of failing even if they were weakened some by removing the bevel.

Maybe someone has already addressed this on the forum before. If so, I hope my calculations are in the same ballpark.

I use #10-24 x 1 1/2" allen head bolts, which don't have a bevel, with a brass washer and recess them into the head block using a reverse spot facer.